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add new github action to execute Stefan's tests #46

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add new github action to execute Stefan's tests

add new github action to execute Stefan's tests #46

Workflow file for this run

.github/workflows/github_tests.yml at 172cfcf
name: Integration Tests & Code Style
on:
push:
branches: [ master, dev ]
pull_request:
branches: [ master, dev ]
jobs:
build-linux:
runs-on: ubuntu-latest
steps:
- name: Checkout Repo
uses: actions/checkout@v2
with:
lfs: true
- name: Checkout LFS objects
run: git lfs checkout
- name: Set up Python
uses: actions/setup-python@v2
- name: Install dependencies
run: |
$CONDA/bin/conda env update --file environment.yml --name base
- name: Lint with flake8
run: |
$CONDA/bin/flake8 src/marbel/
- name: Run tests with pytest
run: |
$CONDA/bin/pytest tests --doctest-modules --cov=src/marbel --cov-report=xml
- name: Convert coverage to lcov format
run: |
$CONDA/bin/coverage lcov
# - name: Send coverage report to Coveralls
# uses: coverallsapp/github-action@master
# with:
# github-token: ${{ secrets.GITHUB_TOKEN }}
# path-to-lcov: "coverage.lcov"
tests-functional:
runs-on: ubuntu-latest
steps:
- name: Checkout Repo
uses: actions/checkout@v2
with:
lfs: true
- name: Checkout LFS objects
run: git lfs checkout
- name: Set up Python
uses: actions/setup-python@v2
- name: Create conda env
run: |
conda create -n marbel python=3.10 r-base
- name: Install the package
run: |
pip install -e .
- name: Simulate reads
run: |
marbel --n-species 3 --n-orthogroups 10 --n-samples 2 4 --library-size 5000 --outdir run_spec10_orth200_samp5-10/
- name: Create conda env for tests
run: |
conda create -n marbel-tests scikit-bio
- name: Execute functional tests
run: |
conda activate marbel-tests || true
echo $CONDA_PREFIX
python tests/tests_functional.py run_spec10_orth200_samp5-10/